Disassembly of DNA-ligands, including DNA-methylene blue (MB) complex and DNA-Co(phen)(3) (3+) complex on mica surface, were investigated by atomic force microscopy (AFM). The disassembly of these complexes occurred after they were immersed in ultra-pure water. AFM results showed that the disassembly depended strongly on bridge ions that were used to immobilize the complex onto mica surface, DNA species and ligands. When Mg(2+) was used as the bridge ion, the DNA-MB complex was completely disassembled because of the weak interactions between Mg(2+) and DNA's bases or mica surface. Although if Co(2+) was used as the bridge ion, the disassembly of the DNA-MB complex mainly depended on the species and shape of DNA. For plasmid DNA pBR 322, plasmid DNA pUC 18 and the linear DNA pBR 322/PstI, the degree of disassembly was gradually increased. Whereas if Co(phen)(3) (3+) was chosen as the ligand, the disassembly of the DNA-Co(phen)(3) (3+) complex was almost blocked because Co(phen)(3) (3+) could hardly diffuse into the ultra-pure water. This obtained information may be useful for practical application of the AFM imaging of biological molecules, especially in liquid.